Homo erectus and other archaic hominids likely interbred with early Homo sapiens

These GEITP pages have often included the topic of Homo sapiens evolution and diaspora (migration out of Africa, then across the world), because it touches on the topic of gene-environment interactions; over the past ~300,000 years, the modern human genome evolved depending in large part on the environment (diet, climate, wars, pestilence). After DNA-sequencing of Neanderthal preserved fossil material revealed evidence for interbreeding with modern humans, admixture was subsequently discovered between Neanderthals and Denisovans, as well as between Denisovans and modern humans. Intriguingly, there have now been several recent papers providing evidence that ancestors of all three groups interbred — at least on two separate occasions — with even more ancient “ghost lineages” of unknown extinct hominins (early species that walked upright and are regarded as ‘human’, or ‘directly ancestral to humans’).

One “candidate” is Homo erectus — an early hominin who migrated out of Africa by 1.8 million years ago, spread to Asia, Oceania and Europe, and could have interbred with later waves of Neanderthal, Denisovan and modern human ancestors. The new genomic studies rely on complex models of inheritance and population mixing, and attempting to establish the precise identity of such hominins, as well as when and where these interbreedings occurred. The gold standard for detecting interbreeding with archaic humans — is to sequence ancient DNA from fossils of the archaic group, then look for traces of it in “modern genomes.” Researchers have done just that with Neanderthal and Denisovan genomes from samples as old as 200,000 years ago from Eurasia. Because no one has been able to extract full genomes from these more ancient human ancestors, population geneticists have developed statistical tools to find unusually ancient DNA in genomes of living people.

A research team from Univ of Utah (see attached editorial; original article in Sci Advanc 21 Feb 2020; 6 (8): eaay5483) also reported finding such “stretches of ancient DNA” in the genomes of different human populations — including Europeans, Asians, Neanderthals, and Denisovans. Researchers tested eight scenarios of how genes are distributed before and after mixing with another group, to see which scenario best simulated the observed patterns. They concluded that ancestors of Neanderthals and Denisovans — whom they call “Neandersovans” — interbred with a “super-archaic” population that had separated from other human lineages ~2 million years ago. Likely “candidates” include early members of our genus, such as H. erectus or one of its contemporaries. The interbreeding most likely happened outside Africa, because that is where both Neanderthals and Denisovans had emerged, and the illicit sex event could have taken place at least 600,000 years ago.

More recently, a report from UCLA identified signs of a separate, more recent episode of interbreeding. Looking at four subpopulations in West Africa (data that exist in the 1000 Genomes Project, a catalog of genomes from around the world), researchers found numerous nucleotide variants not seen in Neanderthals or Denisovans — and concluded that the best explanation was that these gene variants “arose from an archaic, extinct human.” This ghost species may have been late H. erectus, H. heidelbergensis, or a close relative. One or more late-surviving members of this ancient group likely mated with ancestors of living Africans sometime in the past 124,000 years — according to what the modern genomes suggest. Another paper (Science 31 Jan 2020; p. 497) reported Neanderthal DNA in living Africans, likely from migrations back to Africa by early Europeans who carried Neanderthal DNA. It is speculated, however, that some of this archaic DNA detected in Africans may have originated from Neanderthals, but most is from an older ghost species. In conclusion, a whole lot of hanky-panky has been going on between hominin sublines over the past 2-4 million years. For more tantalizing stories about clandestine sex long ago — please examine the attached editorial. 😊


Science 21 Feb 2020; 367: 838-839

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